If the flywheel was machined flat (which it should be), maybe it was worn enough prior to disassembly to provide release clearance for the disc, but the linkage adjustment should take care of it. Are you 100% sure that the release arm is in the right position? Mounting the flywheel farther back (shim between crank flange and flywheel) likely won't help at all, but spacing the pressure plate back with washers should compensate, but will reduce clamping pressure on the disc.
